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    syf-1 Pre-mRNA-splicing factor SYF1 [ Caenorhabditis elegans ]

    Gene ID: 171970, updated on 9-Dec-2024

    Summary

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    Official Symbol
    syf-1
    Official Full Name
    Pre-mRNA-splicing factor SYF1
    Primary source
    WormBase:WBGene00016837
    Locus tag
    CELE_C50F2.3
    See related
    AllianceGenome:WB:WBGene00016837
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Caenorhabditis elegans (strain: Bristol N2)
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
    Summary
    Predicted to be involved in generation of catalytic spliceosome for first transesterification step. Predicted to be located in nucleus. Predicted to be part of Prp19 complex; U2-type catalytic step 2 spliceosome; and post-mRNA release spliceosomal complex. Is expressed in several structures, including intestine; nervous system; pharynx; tail; and vulval muscle. Orthologous to human XAB2 (XPA binding protein 2). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See syf-1 in Genome Data Viewer
    Location:
    chromosome: I
    Exon count:
    7
    Sequence:
    Chromosome: I; NC_003279.8 (3877063..3880743)

    Chromosome I - NC_003279.8Genomic Context describing neighboring genes Neighboring gene C-type lectin domain-containing protein Neighboring gene Ubiquitin-like modifier-activating enzyme 5 Neighboring gene Protein SYS1 homolog Neighboring gene CCHC-type domain-containing protein Neighboring gene Antibacterial factor-related peptide 2 Neighboring gene Antibacterial factor-related peptide 1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003279.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo. Du Z, et al. Dev Cell, 2015 Sep 14. PMID 26321128, Free PMC Article
    2. A protein domain-based interactome network for C. elegans early embryogenesis. Boxem M, et al. Cell, 2008 Aug 8. PMID 18692475, Free PMC Article
    3. SIN-3 acts in distinct complexes to regulate the germline transcriptional program in Caenorhabditis elegans. Robert VJ, et al. Development, 2023 Nov 1. PMID 37818613, Free PMC Article
    4. Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis. Xiao L, et al. Cell Syst, 2022 Aug 17. PMID 35882226
    5. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Simonis N, et al. Nat Methods, 2009 Jan. PMID 19123269, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by WormBase

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in generation of catalytic spliceosome for first transesterification step IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Prp19 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of post-mRNA release spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    Pre-mRNA-splicing factor SYF1
    NP_491250.1
    • Confirmed by transcript evidence

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003279.8 Reference assembly

      Range
      3877063..3880743
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_058849.10 → NP_491250.1  Pre-mRNA-splicing factor SYF1 [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_491250.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      P91175
      Conserved Domains (3) summary
      COG0457
      Location:526 → 704
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:362 → 391
      TPR; TPR repeat [structural motif]
      cl18945
      Location:655 → 701
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    Nucleotide Protein
    Heading Accession and Version

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